Return of Darkness
by Khrow
Summary: Set two years after Into Darkness, Admiral Marcus' predictions had come into fruition . The Klingon had started a war, and the Federation was losing. With Star Fleet's options dwindling, one of their special agents decides to take drastic measures. The only hope, for both Star Fleet and the crew of the Enterprise, may be to once again join forces, with a dangerous foe. KhanXOC
1. Chapter 1

I

He slept, sound and alone, locked away, deep within the research and diagnostics department of Star Fleets Section 31. Gun shots and explosions echoed from behind those closed doors. The cryo chambers rumbled against the immaculate linoleum floor. It was dark, and cold inside the room; when the doors finally opened, the sterile smell quickly dissipated with the influx of billowing smoke.

A figure stood in the doorway, its shadow cascading down over the sleeping men and women within. The visitor cautiously took a step inside; first one step, then another. There wasn't much time. In haste, gloved fingers pulled back the black hood, revealing a tussled mane of raven tendrils, and emerald green eyes. Her skin was a light cream color, cheeks rosy from exertion, and stained with smudges of soot and dirt. She was dressed; battle clad, head to toe, in the finest of Star Fleet's combat gear. Everything from slip resistant treat boots, to damage mitigating body armor. Her legs, hips, and arms were adorned with weaponry; mostly knives and daggers of varying size. She nonchalantly placed her hands on her hips, surveying the room.

A second explosion went off, this one much closer than the last, and it sent the unknown trespasser reeling into the frozen tombs that lay perfectly in line with the rest; bracing against the cold steel. Her fingers wiped away the fog from the window, revealing the identity of the sleeping individual within. Their faces, mere inches apart, were separated by just a thin sheet of glass.

It was a man; handsome, with strong features. His mouth was broad and exaggerated, nose long and narrow, and his eyes, even though closed, she knew there were a miraculous blue. Her lips curled into a smile as she discovered the luck of her fall. The man who slept so stoically within the chamber was Khan, and she had come to awaken him.

It wasn't a difficult procedure, but it was specific, and time consuming. Unfortunately, time was not on her side. She hurried and entered the initiation codes on the console, which was now collecting droplets of moisture from the rooms sudden temperature change. Under conventional circumstances, it would require a hospital and a full medical team in order to successfully revive a "normal" human being. These were not conditional circumstances, and Khan was most definitely not a normal human; however, there was still a margin of risk.

The tube hissed, and the decompression phased commenced. He had only been asleep for two years, since his last awakening, and the young woman was banking on his body's super human abilities, combined with the minimal time spent in coma, to aid in a successful reanimation. As the chamber began its lengthy process, the woman rose to her feet. Her hands slid gingerly down the sides of her hips; fingers interlacing with the handles of two large daggers. The battle was coming to her, and she had fifteen minutes before the process was complete. And even longer still, until Khan himself awoke completely. She took a breath. The weighted footsteps of Klingon warriors were right around the corner. She readied her weapons. There were fifteen, or twenty of them, easily; but, even then, she didn't have the sense enough to be afraid.

The world around her, and even time itself froze, as the first of the Klingon arsenal stepped through the open doorway. Their large and muscular frames appeared even more daunting with the eerie glow of frolicking fire behind them. Before the intruder's had a chance to assess the situation, or the threat this women presented, she flung her right hand forward, expelling one of her daggers deep into the skull of a single opponent. The body dropped, shaking the floor viciously with its weight. Within seconds his comrades charged forward, seeking to avenge their fallen brother. She followed suit, boldly running into battle. The woman fought, just as mercilessly as they, her blades taking life after life, without remorse. One, two, three, four…after twelve, she had lost count of exactly how many Klingon were slain. And just as it seemed as if she was making progress, another handful of reinforcements would filter in. She wasn't sure how long this had been going on, but she understood the strategy. They meant to wear her down, and they had the strength and numbers to do so. It was a game…

Within another couple of minutes, they had accomplished their goal; she was worn, and her movements had become careless. One of the Klingon warriors lashed out, exploiting her exhaustion, he landed a swift kick to her abdomen. The steel tipped boots sent shock waves into her frame, breaking and cracking several ribs. Gasping as the air was violently forced from her lungs, she instinctually fell to her knees. Another kick made contact with her jaw, fracturing bone and sending her fragile body into a set of cryo tubes. Her head hit the metal casing with a startling crack. Disoriented, she slumped to the side, a small pool of blood forming around her agape mouth. Her eyes squeezed shut as she forced her body to move. Agonizing pain shot down every limp, and into her spine.

One of the Klingon casually approached; he leaned down and locked his claw like hand around her throat. She was lifted effortlessly into the air, coughing and frothing foamy, pink sputum over his fingers. The young woman couldn't see his eyes, no, there were no eyes; just a vacant, expressionless helmet.

The Klingon laughed. "puq HoS SoH. tuHmoH pagh Quj vay' nI'qu' 'oH.…"  
_"You are a strong child. It is a shame we cannot play any longer."_

"veS wej Qap" Her voice was raw, barely audible from the crushing grip on her neck.  
_"You will not win."_

The Klingon laughed again. She could feel her heart racing, thumping against her temples. A dizzying, almost intoxicating wave passed over, stemming from the lack of oxygen. Everything became blurry and dim. She felt another hand, this one covering her face; the fingers crushed into her cheeks and temples. Her teeth clenched when the sound of cracking bone echoed within her head.

It was over, all over. Her arms fell limp at her sides as blood tricked from her ears and nose. Everything became a haze. The world and all things in it, her pain and agony, even the very weight of her being was dissipating. She was drifting into a peaceful unconsciousness; and yet, some horrid noise intruded, it was familiar, violent. The vice of stone that was clamped to her head suddenly released. She felt herself hit the floor, sprawled out like a rag doll against the refreshingly cool tile. She was heavy, all over. Her body had come back to her with its aches and pains and choking groans. She felt herself being lifted, cradled against a warm, protective body.

"Oh, my dear Lydia…" The voice, condescending in nature, brought a sigh of relief from her lips. "…always biting off more than you can chew."

She wanted to cry out his name, she wanted to say it with every fiber of her being. She wanted him to acknowledge it, to confirm his identity, his existence…that she was really in his arms, and this wasn't some dream before leaving this world; but, she couldn't. The darkness had come, that sweet, gentile veil of nothingness, pulling her under; Silence.


	2. Chapter 2

II

The sun was high, light falling in dusty shafts from the partially blinded windows. Warm rays sprinkled across the face of a sleeping woman; contouring across her cheek bones and fanning out in golden shimmers over her matted lashes. The room was relatively dim, amidst only the bed itself, and a single chair. In the corner sat an array of medical equipment; used syringes, surgical tubing, scissors, and a pile of bloodied gauze. Her clothing had been removed, cut to pieces, and discarded carelessly in the same pile.

It was Lydia who slept soundly under the clean, cotton duvet; and Khan, who rested in the aluminum, cusp shaped chair beside her. His keen eyes studied the gradual rise and fall of her chest, with every gentle breath; which for two days, had been severely labored. For four days total, he monitored, and nursed her back to health; this fragile woman, the sole member of Star Fleet that he didn't despise with every fiber of his being. She was the only one who ever treated him like a human, like someone who mattered, instead of a savage animal. She never once showed him an ounce fear, nor sought to control him, or exploit him.

After a few moments, he rose, reached out, and lifted Lydia's chin. It was just enough of an elevation for her lips to part and stir a sigh from his sleeping patient. The tame sound made his mouth purse. He gazed over her features, at her ebon hair that lay long and wavy, curling around her neck and shapely shoulders. A few strands strayed, haphazardly placed across her forehead. Khan's thumb traced over the contour of her lips; they were soft, and supple, and healed beautifully, thanks to his blood.

His fingers continued their route along the curvature of her face; stopping to press firmly against the Maxilla. There were no longer any broken bones, or bruises, to stain her cream colored skin, and this pleased him.

Khans methodical prodding continued, massaging her neck, smoothing his hands along her collar bones, and tenderly appraising the structure of her rip cage through the sheer cotton sheets. Lydia groaned. His medicinal treatment caused her to stir; her silken lashes fluttering open. Lydia's eyes squinted against the morning light and she lifted a hand to shield her face. When her vision adjusted, she was startled, but relieved, to see her protector looming above.

"Khan…" His name was a breathless gasp, and she swallowed in an attempt to soothe the dry, rawness of her throat.

Khan watched her eyes open, and close a few more times. He could tell she was fighting off a minute case of muscular atrophy. She took a moment, wiggling her fingers, and toes. Nothing seemed too out of the ordinary, and aside from the grogginess, Lydia felt healthy.

Khan calmly sat down on the bedside, his shoulders pivoted in her direction. Lydia found a great deal of comfort in this; in his closeness, and how deliberately temperate he was. Everything was slowly coming back to her, in small, painful fragments.

"I've contacted the Enterprise, they are on their way to come and get you." Khan's voice was stoic, and emotionless.

Lydia lowered her eyes; his words left a sinking pit in her stomach. "What about you…?"

Khan said nothing; He appeared to be deep in thought.

"Khan, you have to come with me…" She immediately sounded desperate, hoping he understood how truly dire the situation was.

"I don't have to do anything…" Khan's left hand reached out to bite into the soft flesh of her cheeks; forcing her eyes to look at him. "What you did was foolish. You could have been killed…" His tone was reprimanding in nature.

Lydia flinched, but remained relatively still; the might of his hand alone was enough to keep her entire body stationary. It was like steel, wrapped in exquisite velvet. Khan pulled her close, until she was nearly sitting upright. Lydia felt the soft fabric of the blanket slide along her chest, slipping with each inch as she was guided away from the comfort of the pillows; yet, she made no effort to recover it, or cover her bare chest. His calculating visage scrutinized every detail of her face. From her red, flushing cheeks, to her pressed and pouting lips; lips, just centimeters from his. She felt the heat of Khan's breath; it tantalized her skin with every word he spoke.

"You know who I am…_what_ I am…" Khan's jaw widened, emphasizing his inquiry. "You, of all people should know what I am capable of…yet, you risked your life to awaken me? Quite the gamble."

Khan's proximity was dizzying; the forceful presence of his body, his cold and passionate stare; it was almost too much.

"You saved my life." Lydia swallowed. "I know there's a good man in there, somewhere…"

Immediately Khan's hold liberated. He appeared shocked by her response; however, he allowed this lapse in character only for a brief second, and then collected his composure.

"A good man…" He mused, becoming somber; he crooked his head and shifted his gaze to the window.

"Admiral Marcus-"

Khan immediately cut her off, hissing against his teeth. "Don't say his name to me."

Lydia shrank back. She could feel her guilt rising, like a brick in her stomach. She reflected briefly on their past together. She had worked closely with Khan for a year, both on the development of the U.S.S. Vengeance, and together on missions of espionage. "Khan, I'm sorry for what he did…and I'm sorry for not stopping him."

She reached out, both hands cupping the sides of his face, gently turning his head towards her. For the moment, Khan allowed this. "We've lost Starfleet headquarters, our surrounding outposts have been disassembled, and we're scattered and unorganized across space. We need a warriors mind, a leaders mind…your mind. We cannot defeat the Klingon without your help…"

She wanted to tell him that it wasn't all that was needed; that _she_ needed him; that _she_ wanted to save him, and his people; that she needed to somehow rectify her past mistakes. But she couldn't. She felt weak, and undeserving in his presence.

His face grew cynical, yet amused. "Would your valiant and noble Captain Kirk be able to put my past discrepancies aside? The law abiding and intelligent, Mr. Spock, can he truly embrace the violence required to win this war; Even if it means the entire genocide of a race; The Klingon race?"

Lydia knew the answers to his questions; they were poisonously rhetorical. "So you won't help us." It was more of a statement, than a question, a realization of hopelessness.

"This isn't my war." Khan sensed her dejection, and slowly leaned backwards, pulling away. He felt the softness of her fingers brush his chin as they fell. Khan's right hand gently caught hers, massaging his thumb against Lydia's knuckles, marveling at the softness of her skin.

His rough, yet benign touch was oddly soothing, and Lydia couldn't help but smile, just a little. "It feels good to see you again…"

Khan said nothing, but some part of him seemed at peace.

They remained like this, solemnly sharing each other's company, for what felt like an eternity, before Khan offered a reprieve from the silence.

"They're here." He could feel the humming vibration of an aircraft; judging from its sound, most likely the Peregrine. A small ship, commandeered, that the Enterprise used to land while surveying planets.

Lydia felt an unnerving pressure in her chest as he left the bedside. She could hear Khan beside her, gathering things, and preparing for his departure.

Khan was cloaked, with the hood pulled up over his head and his bag slung across his left shoulder. He wanted to leave…needed to leave; but, for some reason, Khan felt a dull, aching feeling, pulling at his chest from the inside; the same feeling he had, when he considered his crew. His teeth clenched hard, knowing all too well what was stirring.

"In three days, meet me on Sarona VIII; there is a lounge, I'm sure you're familiar with it. I'll make contact you there."

Lydia's head snapped up, wide eyed and hopeful. "Where are you going?"

"I am going to get my crew; we will need them if _you_ intend on winning this war."

"Your crew…they're alive?"Lydia felt a wave of relief rush over her.

"Three days. Sarona VIII." Khan ignored her question, offering the petite woman a parting glance; one last look at the face he begrudgingly found so beautiful, and then he was gone.

Lydia sat there, staring at the chair beside her, listening to the hurried footsteps running down the hall. They were mere minutes apart, and how Khan had eluded them, she didn't know. Modestly, she pulled the sheets up to her shoulders, just as her Captain barged into the room.

"Lydia!" It was Kirk; he had his phaser in hand and he was scanning the room upon entry. He called her name with such a childish air of excitement.

Not far behind him was Spock; a little more nonchalant in his heroics. "Lieutenant Frost, I see you are alive, and well."

"Where is he?" Kirk almost barked the order. He was frenzied as he turned, and poked his head out of the doorway to stare down the hall.

"He's gone…" Lydia didn't make eye contact with either of them.

"So it _was_ Khan, after all?" Spock's eyes remained steadfast on Lydia. He was holding a small satchel in his left hand, and approached the bed cautiously. "Lieutenant Uhura's auditory skills are truly unmatched."

"Yes…" Lydia watched as Spock set the bag down beside her. She took the offering, with a small nod of gratitude, and sifted through its contents.

"He was here, and you just let him get away?!" Kirk appeared frantic, focusing so hard on the idea of losing Khan that he neglected to take notice of the situation at hand.

"He saved my life." Lydia's response was almost venomous, shooting Kirk a glare that could melt ice.

Spock, however, was a little more discerning than his captain. He immediately noticed the discarded medical supplies in the far off corner, as well as Lydia's bloodied and dismembered attire. "Judging by the lack of advanced medical equipment, and the mass of tools used in the process…he went through a great deal to ensure your survival." Spock paused, turning his head inquisitively on angle. "Why?"

"I…I don't know…" Lydia removed articles of clothing from the bag: black pants, the standard issued black Starfleet uniformed shirt, undergarments, gloves, and a scarf that doubled as a cowl.

Spock looked down to the chair; it was placed so close to the bed, that whoever was sitting in it was well within reach of its sleeping occupant. A detail he found to be less than just 'ironic'. Draped over the chair was a black leather jacket, and on the floor beneath it, a pair of black combat boots. Neither of which were stained with blood…a pattern that would not fit given the circumstance.

As Kirk tried his 'hardest' not to peek, Lydia dressed, and Spock's mind went to working a mile a minute. Nothing here seemed to fit. Khan was a man who cared only for himself, and his crew, and he had harbored an intense amount of distain for anything affiliated with Starfleet. Why then, would he save Lieutenant Frost? The moment Khan proceeded to cut her uniform from her body; his adept eyes would have caught that infamous symbol. He would have known she was a part of Starfleet, and should have ender her life, right then and there.

"Lieutenant Frost, what aren't you telling us?"

"Spock, I don't follo-"

"But I think you do. Why did Khan save you? Why would Khan, a man bent on the entire destruction of Starfleet, save one of its own? Furthermore Lieutenant, how did you even come into contact with him?"

"Lydia…" Kirk's tone quickly became more caring, and he gently squeezed her shoulder, offering some comfort, and support. "What happened?"

Lydia froze. "I'm not a Lieutenant…."

Both Spock and Kirk seemed perplexed by the initial randomness of her statement.

"I am an Agent for Section 31."

"Seciton 31…" Spock whispered the phrase, coming across it only briefly in his education and then again during their confrontation with Admiral Marcus. "…So, it was rebuilt…"

"Yes. Section 31 is an organization dealing in both defense and intelligence. In essence, it is a security force, created to do what is necessary to protect Starfleet from outsider harm."

"What is necessary?" Kirk raised an eyebrow.

"Yes. When the Klingon declared war, many of the scientists, and agents went into hiding; some have been captured and killed by the Klingon. The few of us who remained were assigned to ships; our credentials were spun to fit the necessities of each ships needs in order to board and become an integrated part of the crew. I was assigned to the Enterprise; it only made sense given my experience. We bend the rules during times of extraordinary threat." Lydia's statement was cold, mechanic, as if it were practiced, over and over until perfected. "During my time as an agent for Section 31, I serve as an undercover combat operative. My specialization is espionage. It's true, that Admiral Marcus had a hand in the initial awakening of Khan; but, I was in charge of supervising the procedure…I woke him…Marcus simply gave the order." Lydia paused; it was Spock alone who took notice of her subtle change in tone, there was a hint of sadness within her words. "We worked together on the development of the U.S.S. Vengeance. In addition, I was responsible for supervising him. During one of our missions, Khan went rogue…he eluded me…and I suppose you know how the story ends."

"Lydia, how much do you know about Khan?" Kirk posed the question; even after their initial run in with Khan, two years prior, there was still so much about the man that was left in the dark. Section 31 refused to offer any information, even after his recapture.

"I know everything." Lydia turned her back to them both, slowly walking to the window. Her fingers parted the blinds, allowing her to gaze out over the abandoned city. "Khan Noonien Singh, a genetically augment human being, born in 1970, and designed to be perfect. Twice the intellect, a fifty prevent greater lung efficiency, immense physical resilience, and strength five times greater than our own. He even posses heightened senses. Khan truly is the best weapon against the Klingon…My apologies Captain…but my job is to protect Earth, and the Federation, at all costs…so…I did what was necessary."

"You awoke Khan…" Spock's eyes narrowed.

"Section headquarters has always been at the very top of the Klingon hit list; their only problem was they couldn't find it. They want our weapons, and our science. Even worse, they want Khan and his people. The Klingon had dabbled in species augmentation before, but were far from successful. Imagine a war, not only against the most brute of races, the most physically resilient, and relentless; but, against the most tactically sound as well. If the Klingon managed to create an alliance with Khan, and his crew, they would have the combined intellect, and strength to annihilate us all."

Spock immediately went on the offensive. "Agent Frost, you are assuming that Khan can be trusted; when, he has already proven to us that he cannot be. What would prevent him from turning on us again, or worse yet, aligning with the Klingon?"

"That won't happen…" Lydia's voice grew soft.

"How do you know? Furthermore, you have still yet to clarify a few things. You're not only a member of Starfleet, but an agent for Section 31. Knowing those facts, why would Khan opt to save you, let alone, join forces with us again?"

"Perhaps he's not as bad a man as you both believe."

"I've seen what he can do…" Kirk's brow furrowed together. "Lydia, he has killed thousands!"

Lydia aggressively spun to face them both. "And the Klingon will kill even more! We are at war, _Captain_; Khan is our last hope. The Klingon are stronger, faster, and operate completely without rules or regulations. We are losing….we need to even the playing field. As much as I hate to admit it, Admiral Marcus was right…Khan is the key to winning this war."

Spock could feel the two worlds within him in conflict. To some degree, Lydia's logic was sound, and if Khan could be harnessed, winning the war was likely. However, he couldn't help but feel the burden of every risk involved. What would happen if Khan turned on them? They were fortunate enough to put an end to his rampage the last time they met; would they be so fortunate again?

Kirk struggled to refute her argument as well. After all, he himself used Khan to infiltrate the U.S.S. Vengeance. Kirk took a breath. "Lydia…were did Khan go?"

"To gather information on the Klingon fleet…" Lydia swallowed hard against her lie. She knew both Kirk, and Spock would strongly oppose the awakening of Khans crew. "He will rendezvous with us in three days on Sarona VIII."

"What do you think, Spock?" Kirk looked to his all knowing friend for support.

Spock hesitated. "You're going to go through with this, with or without us. Am I correct Agent Frost?"

"You are correct, Commander Spock." Her voice harbored no uncertainty.

Spock shifted his gaze to Kirk, producing an inquisitive demeanor. "Captain, I refer to your good judgment. After all, you are the self proclaimed expert on all things…unorthodox."

Kirk shifted his stance, and offered Lydia a playful smile. "Well, I sure as hell can't let you do this alone. It looks like we'll be setting a course for the Sarona system."


End file.
